TmPrime is a computer program to design oligonucleotide sets for LCR- and PCR-based gene synthesis to construct man-made DNA sequences by assembling pools of oligonucleotides.
The program divides the long input DNA sequence based on the user specified melting temperatures and assembly conditions, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences, and potential formation of secondary structures in a csv (comma separated values) file which can be read by Excel or Open Office.
You can either design oligonucleotides with or without codon optimization. For quick start, please check the following examples designed without codon optimization ( S100A4, PKB2 or GFP).
Calculation with codon optimization
Calculation without codon optimization
Calculations so far: . Last modified: April 16, 2009.